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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Possible feature request #1612

Open ValWood opened 3 years ago

ValWood commented 3 years ago

HI @cmdcolin

We had a PomBase user ask for "summary statistics" for a region (e.g. number of genes, origins, GC content or whatever). Is this something that JBrowse might provide in future? Or is it already available and I didn't find it?

Best

Val

cmdcolin commented 3 years ago

I don't think anything particularly exists like this currently. There are some stats in the tracks that have been loaded with flatfile-to-json.pl in the "About this track" dialog but nothing for for a region that someone is looking at. There is also some code internally that calculates a couple statistics but it is not exposed to the user. This is an idea we could keep in mind as we are developing jbrowse 2!

ValWood commented 3 years ago

Excellent! There is a similar feature in Artemis, which we use for curation, but this is the first user request we had for this. If implemented, let us know and we will announce to the pombe community. Thanks...

cmdcolin commented 3 years ago

Good to know. We have had some discussions with artemis team and have started some work on curation in jbrowse too....this is interesting to know. The more info we can know about what feature the user is interested probably the better, but if you are not sure that is ok too.

CC @garrettjstevens @elliothershberg

ValWood commented 3 years ago

They just want to be able to select a region or subsequence and have a tally of how many genes/annotated features are in that region, and other summary statistics like GC content. I guess this will become more popular as people try to evaluate the contents of different TADs for example. It will only work for tracks with annotated features which correspond to specific SO terms.

Artemis allows you to select a subsequence, then there is an option under the view menu called "overview" which does this, and the GC content can be obtained from the graphs, but it would be nice of sequence stats were also included in the overview summary.